BluVision - an image analysis framework

for plant-pathogen interactions

Stefanie Lck, Patrick Schweizer and Dimitar Douchkov
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrae 3,
06466 Seeland, Germany

Phenomics ABC Powdery mildews BluVision Framework

Phenotype - combination of an Fungal disease that affects a wide range We have developed the BluVision
organism's observable characteristics of plants. Micro- and Macrophenomics
Phenotyping - observation and Barley and wheat powdery mildews Framework. The system is build to
characterization of the phenotype (Blumeria gramminis f.s. hordei resp. cover the complete life cycle of the
Phenomics high-throughput tritici) are important pathogens and powdery mildew fungus by collecting
phenotyping scientific models together with their hosts and analyzing image data from three
Micro- and Macrophenomics a new barley and wheat. key developmental stages but it can be
term meaning phenomics by means of applied also to other plant-pathogen
microscopy and macrography techniques interactions.

Macrobot - an Zeiss Axio

image acquisition Scan.Z1 a
robot for MTP high-throughput
format samples microscope
Photos: apsnet.org scanner
Separate 16-bit monochrome The key stages in the powdery mildew Multidimensional
images for each channel (R, interaction with cereals (central figure) image files (CZI)
G, B, UV) are subject of tree different phenotyping
BluVision Macro system parts of the BluVision BluVision Haustoria
Automated quantification Framework: BluVision Haustoria Automated haustoria classification
of infection symptoms. (right). Early type of interaction scored 1 based on convolutional neural networks
day after inoculation (dai); BluVision ROIs (reporter expressing cells) were
Hyphae (lower panel). Intermediate segmented and a convolutional neural network
Plate with infected interactions scored at 2-4 dai; BluVision (CNN) was trained on 100.000 examples to
leaf segments (RGB classify the present of haustoria formation
composite)
Macro (left). Late interactions scored at
5-7 dai. inside the cell.
Leaf segmentation C C C P
R R R R
O O O o F
G L L L
N N N o C
B U U U
V V V l

32x32 64x64 128x128 2x2

0 dai Initial contact

Disease Validation

segmentation Training

Prediction (leaf wise) Man vs.CNN

0.60
r=0.98
Automated vs manual disease rating 0.50
100
5 dai Visible pustules, sporulation 1 dai Haustorium formation
Manualy estimated infected area [%]

90 0.40
r=0.95
Automatic SI

80
70 0.30

60
0.20
50
40
0.10
30
20 0.00
0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45
10
0 3 dai Secondary hyphae Manual SI

0 20 40 60 80 100
Automatically estimated infected area [%] SI (Susceptibility Index) = [infected cells) / [total reporter exp. cells)

Zeiss BluVision Hyphae - Automated fungal colony detection and morphological measurements.
Axio Scan.Z1
True and false positive objects per
700 sample
Adaptive threshold 600
False positive
segmentation and True positive
Multidimensional 500
Objects count

contour finding followed

image files (CZI) by a colony classification 400
based on PFTAS, 300
Haralick and geometric
200
features.
RGB 100

0
Image Samples
segmentation
Classification

Macrobot on Youtube:

mahotas
This work was performed within the
German-Plant-Phenotyping Network which
is funded by the German Federal Ministry of Poster download:

Education and Research (project

identification number: 031A053) and IPK
Gatersleben.
We gratefully acknowledge the support of
NVIDIA Corporation with the donation of the http://labtools.ipk-
gatersleben.de/poster/poster_Euro
SciPy2017.pdf
Titan X Pascal GPU used for this research.